Sequencing of S and N genes of SARS-CoV-2 strains circulating in Cuba during March- September 2020

Objectives: The first confirmed cases of COVID-19 in Cuba were reported on March 11, 2020, followed by multiple introductions of infected travelers from Europe, America, and Asia. This work aimed to characterize the SARS-CoV-2 strains circulating in Cuba from March to September 2020 by partial nucleotide sequencing of the S and N genes. Methods: Between March and September 2020, 38 nasopharyngeal exudates from 38 SARS-CoV-2 patients were received at the National Reference Laboratory for Influenza and Respiratory Viruses at the Institute of Tropical Medicine “Pedro Kourí” (IPK). The Sanger sequencing method was used to amplify and sequence a 2539 bp fragment of the spike gene (from position 22020 to 24550) and a 370 bp of the nucleoprotein gene (from position 28340 to 28710). The GISAID database was used to identify the mutation profile of both fragments, and phylogenetic analysis was used to confirm the clades. In addition, clinical and epidemiological data from patients were gathered. Results: There were 34 and 25 sequences from S and N genes, respectively. In 21 of them, both genes (S and N) were available, whereas, in the remaining 13 and 4, only S or N sequences could be obtained. Based on the presence of the D614G mutation, 32 samples (84.2%) were classified as clade G of SARS CoV-2, and two were classified as Wuhan. No classification was possible in the remaining four (where only the N sequence was available). In one sample each, five different mutations were detected in clade G samples: L517F, L517X, N603T, A846V, and E281V. The 26 N sequences obtained were 100.0% identical to those circulated in most countries. The G30R mutation was detected in an infected patient in Cuba. Fourteen of the 38 patients studied were imported cases. The first three cases detected with COVID-19 in Cuba were clade G and originated in Italy. Ten individuals were asymptomatic, four presented severe forms of the disease (two fatal), and the remaining presented mild symptoms. No relationship was observed among the clades or the mutational profile with the clinical features, country of origin, and Cuban provinces. Conclusion: The early establishment of SARS-CoV-2 genetic surveillance in Cuba was helpful for tracking the epidemic. It demonstrated that the SARS-CoV-2 clade G was introduced initially and was the variant that circulated in the country during 2020, although the Wuhan strain was also detected. J Microbiol Infect Dis 2022; 12(3):77-88.